Structure of PDB 1ckm Chain B Binding Site BS01

Receptor Information
>1ckm Chain B (length=317) Species: 10506 (Paramecium bursaria Chlorella virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPN
PVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTV
YLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMD
LASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIY
HTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPN
LRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKT
LLNIEENITIDELLDLF
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain1ckm Chain B Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ckm X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K82 T83 R87 R106 E131 F146 K188 I216 R228 K234 K236 D244 R295
Binding residue
(residue number reindexed from 1)		K72 T73 R77 R96 E121 F136 K178 I206 R218 K224 K226 D234 R285
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.50: mRNA guanylyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004484 mRNA guanylyltransferase activity
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006370 7-methylguanosine mRNA capping

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1ckm, PDBe:1ckm, PDBj:1ckm
PDBsum1ckm
PubMed9160746
UniProtQ84424|MCE_PBCV1 mRNA-capping enzyme (Gene Name=A103R)

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